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Miscellaneous => Related topics => Topic started by: ramon989 on April 20, 2009, 06:28:56 am

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Title: 3DNA version 2.0
Post by: ramon989 on April 20, 2009, 06:28:56 am
Hi,

I've read about version 2.0 of 3DNA. (The website works really nice)
This raises some questions:

1. I sent an E-mail to prof.dr. Olson, but I never get a reply, yet I still would like to use 3DNA v2.0 in the future. Help ?
2. What's new in v2.0 ?
      Perhaps this can be added to the topic on 3DNA v2.0

Regards,
Ramon van der Werf
Ph.D. Student at the Radboud University of Nijmegen, The Netherlands
Title: Re: 3DNA version 2.0
Post by: xiangjun on April 20, 2009, 11:33:53 pm
Dear Ramon,

Thanks for bringing up the issue of downloading 3DNA v2.0. Dr. Olson is the proper contact for further instructions. Rutgers has imposed some licensing policy that is beyond my interest to get a hand on. Here is an excerpt, verbatim, of the message I sent to Dr. Olson regarding the release of 3DNA v2.0, after I uploaded the distribution tarball files for the most common operating systems (that I have access to) to the server in a password protected directory:
Quote from: "On March 16, 2009, in an email to Dr. Olson, I"
It is quite a while since our 3DNA NP paper was published. Over the
time I have received a couple of requests to download 3DNA v2.0
mentioned in our paper. Due to (complicated) license issues, I think
you are in a position to handle this issue. By getting more directly
involved, you would understand better what it means to maintain and
support a software.
As far as what's new with v2.0, it has already been mentioned in http://3dna.rutgers.edu/ (http://3dna.rutgers.edu/). To recap, v1.5 as currently available in http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html (http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html) was compiled 6 years ago that had never been updated. Of course, it still serves the majority of common cases very well, and I have used it as a test case of how robust my original implementation is (which is quite assuring, BTW). Of course, over the years, I have fixed bugs, added new features, and updated 3DNA to handle the remediated PDB files etc, which I have communicated with users on a case-by-case basis. The v2.0 contains an accumulation of all these refinements. More importantly, in writing the 3DNA Nature Protocols paper (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=97), I have added more command line options, new scripts and worked examples (NP_Recipes.tar.gz (http://http://3dna.rutgers.edu:8080/data/NP_Recipes.tar.gz)). Accurately reproducing these examples and understanding how each works, users would see why 3DNA is called 'a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures' . Aren't these sufficient reasons to upgrade?

Xiang-Jun
Title: Re: 3DNA version 2.0
Post by: quraishi on April 28, 2009, 02:08:29 pm
Hi,

I would like to get access to 3DNA v2 as well. I have not used a previous version of 3DNA and so it would be nice to get started with the new version.

Thanks!
Mohammed
Title: Re: 3DNA version 2.0
Post by: mariya on July 20, 2009, 05:57:06 am
Sir
   I have registered in 3DNA forum. Would you please give details about downloading 3DNA  2.0 (i read in 3DNA forum that it requires some license, password etc)
Title: Re: 3DNA version 2.0
Post by: xiangjun on July 20, 2009, 07:28:36 pm
Quote from: "mariya"
I have registered in 3DNA forum. Would you please give details about downloading 3DNA 2.0 (i read in 3DNA forum that it requires some license, password etc)

Please note that registration with the 3DNA forum is unconnected (at least for the time being) with downloading 3DNA v2.0. I have tried hard to make my point simple and unambiguous, so please follow instructions there (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=122).

Xiang-Jun
Title: Re: 3DNA version 2.0
Post by: barth on July 27, 2009, 06:02:05 am
Quote from: "ramon989"
...
I've read about version 2.0 of 3DNA. (The website works really nice)
...
1. I sent an E-mail to prof.dr. Olson, but I never get a reply, yet I still would like to use 3DNA v2.0 in the future. Help ?

Also we would like to use version 2.0, but we are not able to because of the same reasons.

Bart Hooghe,
PhD student bioinformatics,
VIB UGent
Title: Re: 3DNA version 2.0
Post by: xiangjun on July 27, 2009, 07:46:17 pm
Thanks for your interest in 3DNA and for sharing your difficult experience with the user community. Over the past few months, I have received (being CC-ed) dozens of email requests for 3DNA v2.0, and I am just wondering if anyone has a more positive story to cheer up the mode of this thread a bit -- any feedback?

Technically, I have already done everything as far as 3DNA v2.0 itself is concerned. What's leftover is distribution, the final stage of a software product, presumably an exciting experience both to the author and the user community. Rutgers has licensed 3DNA and required that it is distributed in a protected fashion, with user registrations etc. In principle, it is easy to release the tarballs of 3DNA v2.0, which I compiled early this year, automatically through a web-form. Even dealing with each individual user's request manually, on a case-by-case basis, should take no longer than a few minutes. Over the times, I have mentioned to Rutgers several times that distributing 3DNA as widely as possible (with proper measure of protection of intellectual property) is to the benefit of everyone who really cares about the software product, and it is also an obligation per the 2008 3DNA Nature Protocols publication (http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=97).

Xiang-Jun
Title: Re: 3DNA version 2.0
Post by: 1982leoyao on September 22, 2009, 05:31:24 am
发邮件给Dr. Wilma Olson,他又不回,有谁得到并使用了3DNA V2.0?
Title: Re: 3DNA version 2.0
Post by: franpre on April 27, 2010, 10:15:37 pm
Hello everyone, good seeing the forum is quite active on such an specific topic. I want to introduce this software to my Professors at UPR-RP so I guess I will have to tinker around here.
Title: Re: 3DNA version 2.0
Post by: xiangjun on April 28, 2010, 06:54:57 pm
Welcome to join the forum! You (and every subscriber) are welcome to post any question that is related to the 3DNA software package, just remember to follow common-sense rules.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.